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PostPosted: Tue Jan 17, 2017 5:43 pm 
Millimolar User
Millimolar User
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Joined: Tue Jan 17, 2017 4:57 pm
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Hey everyone.

I'm using Chimera 1.11.2.

I used a known pdb model file fetched from the server to generate structural models of several similar protein sequences with the integrated MODELLER script.
Since the known pdb model contains a covalently attached FAD cofactor, I let MODELLER also integrate it into my models (non-water HETATM).

However, I used the known model as well as the generated structural models for substrate/product dockings using the integrated AutoDock Vina script.
When I use the known pdb model as the receptor, everything works fine.
But when I use the structural models as receptors, I receive following error msg:
"Parse error on line 8481 in file "receptor.pdbqt": ATOM syntax incorrect: "Ho" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."
It should be noted that everything works fine, when I generate structural models without the cofactor FAD.

An excerpt of the generated pdbqt responsible for the error:
HETATM 8482 HO3B FAD 524 62.332 67.414 -32.163 1.00 0.00 0.229 Ho
HETATM 8483 HO2B FAD 524 61.112 67.370 -35.434 1.00 0.00 0.218 Ho
HETATM 8484 1H6A FAD 524 68.689 67.444 -38.650 1.00 0.00 0.157 HD
HETATM 8485 2H6A FAD 524 67.993 65.870 -38.318 1.00 0.00 0.157 HD
HETATM 8486 HO2' FAD 524 66.161 59.657 -28.008 1.00 0.00 0.221 Ho
HETATM 8487 HO4' FAD 524 63.764 62.100 -29.206 1.00 0.00 0.231 Ho

So i found that AutoDock needs the "Ho" to be a "HD"? Is this correct? But the problem is that AutoDockVina generates the pdbqt file itself. So why does it generate a file containing parameters "Ho" while it cannot read it in the next step?
Anyways, is there a way for me to circumvent this? I cannot just change the entries within the pdbqt file since the AutoDockVina script always generates a new file/overwrites it in the beginning.

I hope you could understand my problem and maybe u are able to help me.
Thanks i advance!

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